Project 2 (Rapid Gene Discovery) has as its major goal the discovery of the gene(s) whose structure and/or expression are disrupted by individual balanced chromosome aberrations associated with developmental abnormalities of the nervous system, including neurological, behavioral and neuroendocrine phenotypes. In addition, Project 2 will assist investigators from Projects 1 and 3 in applying these strategies to subjects with phenotypes in other systems. Molecular biological methods will be employed in a sequence-based strategy to identify the precise genomic positions of breakpoints on chromosomes involved in apparently balanced aberrations and to determine the sequence of the breakpoints and consequent structure of the rearrangements. In the initial phase of the renewal period, we will implement Solexa-based paired-end sequencing of linking fragments to identify the site of the breakpoint without the need for initial FISH mapping. The potential functional consequences of each chromosomal rearrangement will then be examined. Direct gene disruption, either of annotated genes or suspected transcripts, and the potential generation of fusion proteins will be confirmed by analyses of DMA sequence, RNA expression and protein expression. Surrounding genes potentially subject to a position effect will be prioritized by bioinformatic analysis and analyzed at the RNA level for disrupted expression. Bioinformatic approaches will also be taken to identify potential non-coding RNAs and non-coding conserved sequences that could be affected by the chromosomal rearrangement. Finally, candidate genes/sequences will be validated by examining the loci in collections of patients who express similar phenotypes but who do not display chromosomal disruption. Candidate genie and non-genie sequences will be directly sequenced to determine whether individual sequence variants with function-disrupting potential are identified in patients but are not present on control chromosomes. While itself focusing on driving the characterization of genes causing neurological, behavioral and neuroendocrine phenotypes, Project 2 will also act as a resource for completing these steps in the case characterization for subjects studied by Projects 1 and 3, which will focus on other body systems.